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C

calculateArrayLength(long) - Method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
Calculates the number of long array elements necessary to store the specified number of elements.
calculateBitsPerValue(int) - Static method in class info.bioinfweb.commons.collections.PackedIntegerArrayList
Calculates how many bits are necessary to represent the specified number of different values.
canRedo() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
 
canUndo() - Method in class info.bioinfweb.commons.swing.AbstractDocumentEdit
 
CaptchaDBManagement - Class in info.bioinfweb.commons.servlet
 
CaptchaDBManagement(SQLManipulator, String, String, int, String, int) - Constructor for class info.bioinfweb.commons.servlet.CaptchaDBManagement
 
cascade(int) - Method in class info.bioinfweb.commons.swing.ExtendedDesktopPane
 
cascade() - Method in class info.bioinfweb.commons.swing.ExtendedDesktopPane
 
changedUpdate(DocumentEvent) - Method in class info.bioinfweb.commons.swing.SwingChangeMonitor
 
ChangeMonitor - Class in info.bioinfweb.commons.changemonitor
Basic implementation of ChangeMonitorable.
ChangeMonitor() - Constructor for class info.bioinfweb.commons.changemonitor.ChangeMonitor
 
ChangeMonitorable - Interface in info.bioinfweb.commons.changemonitor
A common interface that can be implemented by classes that track whether they have undergone changes.
CHAR_SET_COMMAND - Static variable in class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.SetsBlockParser
 
CharacterStateSetType - Enum in info.bioinfweb.commons.bio
Enumerates defined token set definitions (e.g.
CharacterSymbolMeaning - Enum in info.bioinfweb.commons.bio
Enumerates defined meanings of single character states in sequence alignments.
CharacterSymbolType - Enum in info.bioinfweb.commons.bio
Enumerates of which type a character symbol may be.
charSequenceToStringList(CharSequence) - Static method in class info.bioinfweb.commons.text.StringUtils
Converts the specified character sequence to a list strings, where each character of the sequence is represented as a single string object.
CharSet - Class in info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus
Stores a label of a part of a sequence (e.g.
CharSet(String) - Constructor for class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.CharSet
 
CharSetNexusFileBuilder - Class in info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus
Builds a Nexus file including information from the SETS block by listening to events.
CharSetNexusFileBuilder() - Constructor for class info.bioinfweb.commons.bio.biojavax.bio.phylo.io.nexus.CharSetNexusFileBuilder
 
childHasFocus(Component) - Static method in class info.bioinfweb.commons.swing.SwingUtils
 
childHasFocus(Composite) - Static method in class info.bioinfweb.commons.swt.SWTUtils
 
clear() - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
 
clear() - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
 
clear() - Method in class info.bioinfweb.commons.collections.ListDecorator
 
clear() - Method in class info.bioinfweb.commons.collections.NonStoringCollection
 
clear() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
 
clear() - Method in class info.bioinfweb.commons.collections.SequenceIntervalList.IntervalInformation
 
clear() - Method in class info.bioinfweb.commons.io.IOProgressListenerVector
 
clear() - Method in class info.bioinfweb.commons.swing.ActionMap
 
clear() - Method in class info.bioinfweb.commons.swing.ListBackedListModel
 
clear() - Method in class info.bioinfweb.commons.text.UniqueNameMap
 
clearMessages() - Method in class info.bioinfweb.commons.log.ApplicationLoggerDialog
 
clearOffscreeImage() - Method in class info.bioinfweb.commons.applet.DoubleBufferedApplet
 
clone() - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
Returns a new instance if this class having the same version numbers and application type as this instance.
clone() - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
clone() - Method in class info.bioinfweb.commons.io.FormatVersion
 
close() - Method in class info.bioinfweb.commons.io.LimitedInputStream
Closes the decorated input stream, if that is currently allowed.
close() - Method in class info.bioinfweb.commons.io.LimitedReader
Closes the decorated reader, if that is currently allowed.
close() - Method in class info.bioinfweb.commons.io.PeekReader
 
close() - Method in class info.bioinfweb.commons.log.TextFileApplicationLogger
Closes the underlying writer or the target file.
CLOSING_TAG_PATTERN - Static variable in class info.bioinfweb.commons.HTMLTruncater
Checks for closing tags, allowing leading and ending space inside the brackets
ClosingNotAllowedException - Exception in info.bioinfweb.commons.io
This exception is thrown by LimitedReader or LimitedInputStream if their close() method is called while closing these streams is prohibited.
ClosingNotAllowedException() - Constructor for exception info.bioinfweb.commons.io.ClosingNotAllowedException
 
ClosingNotAllowedException(String, Throwable) - Constructor for exception info.bioinfweb.commons.io.ClosingNotAllowedException
 
ClosingNotAllowedException(String) - Constructor for exception info.bioinfweb.commons.io.ClosingNotAllowedException
 
ClosingNotAllowedException(Throwable) - Constructor for exception info.bioinfweb.commons.io.ClosingNotAllowedException
 
codeCorrect(String, String) - Method in class info.bioinfweb.commons.servlet.CaptchaDBManagement
 
codeToID(String) - Method in class info.bioinfweb.commons.servlet.CaptchaDBManagement
 
CollectionUtils - Class in info.bioinfweb.commons.collections
 
CollectionUtils() - Constructor for class info.bioinfweb.commons.collections.CollectionUtils
 
colorToHexString(Color) - Static method in class info.bioinfweb.commons.graphics.GraphicsUtils
 
columnAdded(TableColumnModelEvent) - Method in class info.bioinfweb.commons.swing.TableColumnModelAdapter
 
columnMarginChanged(ChangeEvent) - Method in class info.bioinfweb.commons.swing.TableColumnModelAdapter
 
columnMoved(TableColumnModelEvent) - Method in class info.bioinfweb.commons.swing.TableColumnModelAdapter
 
columnRemoved(TableColumnModelEvent) - Method in class info.bioinfweb.commons.swing.TableColumnModelAdapter
 
columnSelectionChanged(ListSelectionEvent) - Method in class info.bioinfweb.commons.swing.TableColumnModelAdapter
 
COMMAND_TERMINATOR - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.hennig86.Hennig86Writer
 
COMMAND_TERMINATOR - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
 
CommandLineReader - Class in info.bioinfweb.commons
Tool class that allows to analyze command line arguments that have been passed to an application.
CommandLineReader(String[]) - Constructor for class info.bioinfweb.commons.CommandLineReader
Creates a new instance of this class.
COMMENT_END - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
 
COMMENT_START - Static variable in class info.bioinfweb.commons.bio.biojava3.alignment.io.nexus.NexusWriter
 
compare(T, T) - Method in class info.bioinfweb.commons.collections.SequenceIntervalPositionAdapterForComparable
 
compare(SimpleSequenceInterval, SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.SimpleSequenceIntervalFirstPosComparator
 
compare(SimpleSequenceInterval, SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.SimpleSequenceIntervalLastPosComparator
 
compare(SimpleSequenceInterval, SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.SimpleSequenceIntervalPositionAdapter
 
compare(StreamLocationProvider, StreamLocationProvider) - Method in class info.bioinfweb.commons.io.StreamLocationProviderOffsetComparator
 
compare(AcceptLanguageEntry, AcceptLanguageEntry) - Method in class info.bioinfweb.commons.servlet.acceptlanguage.QualityComparator
Returns -1 if o1.getQuality() is less than o2.getQuality(), 0 is they are equal and 1 if o1.getQuality() is greater than o2.getQuality().
compareTo(ApplicationVersion) - Method in class info.bioinfweb.commons.appversion.ApplicationVersion
Compares two application versions.
compareTo(AmbiguityBaseScore) - Method in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
compareTo(SimpleSequenceInterval) - Method in class info.bioinfweb.commons.collections.SimpleSequenceInterval
 
compareTo(FormatVersion) - Method in class info.bioinfweb.commons.io.FormatVersion
Returns 0 if major and minor version are equal, 1 if this version is later than the specified one and -1 if the specified version is later.
complement(char) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
Returns the complement of the specified character.
complement(CharSequence) - Static method in class info.bioinfweb.commons.bio.SequenceUtils
Returns the complementing sequence.
ConcatenatedSequenceView<C extends org.biojava3.core.sequence.template.Compound> - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.views
Allows to view multiple concatenated sequences as a single sequence.
ConcatenatedSequenceView() - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
ConcatenatedSequenceView(Collection<Sequence<C>>) - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
ConcatenatedSequenceView(Sequence<C>[]) - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
ConcatenatedSequenceView(Sequence<C>) - Constructor for class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
ConcatenatedSequenceView.ViewedSequence - Class in info.bioinfweb.commons.bio.biojava3.core.sequence.views
 
concatWithOperator(String, String, String, String, String) - Static method in class info.bioinfweb.commons.text.StringUtils
Concatenates two expressions with an operator if both are not empty.
concatWithOperator(String, String, String) - Static method in class info.bioinfweb.commons.text.StringUtils
Concatenates two expressions with an operator if both are not empty.
ConcreteSQLProperties - Class in info.bioinfweb.commons.sql.sqlproperties
Default implementation of the SQLProperties interface.
ConcreteSQLProperties() - Constructor for class info.bioinfweb.commons.sql.sqlproperties.ConcreteSQLProperties
 
ConsensusSequenceCreator - Class in info.bioinfweb.commons.bio
 
ConsoleApplicationLogger - Class in info.bioinfweb.commons.log
An implementation of ApplicationLogger that outputs all messages to System.out and System.err.
ConsoleApplicationLogger() - Constructor for class info.bioinfweb.commons.log.ConsoleApplicationLogger
 
consumeNewLine() - Method in class info.bioinfweb.commons.io.PeekReader
Consumes any one of a line feed '\n', a carriage return '\r', or a carriage return followed immediately by a line feed, if found at the current position of the reader.
contained(String, int, int) - Method in class info.bioinfweb.commons.CommandLineReader
Checks if the given value is contained in the arguments and returns the index.
contained(String, int) - Method in class info.bioinfweb.commons.CommandLineReader
Checks if the given value is contained in the arguments and returns the index.
contained(String) - Method in class info.bioinfweb.commons.CommandLineReader
Checks if the given value is contained in the arguments and returns the index.
contains(Object) - Method in class info.bioinfweb.commons.collections.ListDecorator
 
contains(int) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
Checks whether the specified position is marked by this list.
contains(Object) - Method in class info.bioinfweb.commons.collections.NonStoringCollection
Since no objects are stored in this collection this method will always return false.
contains(Object) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
 
contains(UndoableEdit) - Method in class info.bioinfweb.commons.swing.AccessibleUndoManager
 
contains(JFileChooser) - Method in class info.bioinfweb.commons.swing.FileChooserDirModel
 
containsAll(Collection<?>) - Method in class info.bioinfweb.commons.collections.ListDecorator
 
containsAll(int, int) - Method in class info.bioinfweb.commons.collections.NonOverlappingIntervalList
Checks whether all positions in the specified interval are marked by this list.
containsAll(Collection<?>) - Method in class info.bioinfweb.commons.collections.NonStoringCollection
Since no objects are stored in this collection this method will always return false.
containsAll(Collection<?>) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
 
containsAllNames(Collection<?>) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
 
containsAllNames(Collection<?>) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
 
containsKey(Object) - Method in class info.bioinfweb.commons.text.UniqueNameMap
 
containsName(String) - Method in class info.bioinfweb.commons.bio.biojava3.alignment.SimpleAlignment
 
containsName(String) - Method in interface info.bioinfweb.commons.bio.biojava3.alignment.template.Alignment
 
containsPosition(int) - Method in class info.bioinfweb.commons.collections.SequenceIntervalList
 
containsRect(Rectangle, Rectangle) - Static method in class info.bioinfweb.commons.Math2
Checks if one rectangle is completely contained inside the other.
containsValue(Object) - Method in class info.bioinfweb.commons.text.UniqueNameMap
 
containsWhitespace(CharSequence) - Static method in class info.bioinfweb.commons.text.StringUtils
Tests if the specified character sequence does not contain any whitespace.
ContentExtensionFileFilter - Class in info.bioinfweb.commons.io
An abstract file filter that allows to test the content of a file to determine whether it is accepted by this filter.
ContentExtensionFileFilter(String, boolean, ContentExtensionFileFilter.TestStrategy, boolean, String...) - Constructor for class info.bioinfweb.commons.io.ContentExtensionFileFilter
Creates a new instance of this class.
ContentExtensionFileFilter(String, boolean, String...) - Constructor for class info.bioinfweb.commons.io.ContentExtensionFileFilter
Creates a new instance of this class.
ContentExtensionFileFilter.TestStrategy - Enum in info.bioinfweb.commons.io
Determines the way instances of ContentExtensionFileFilter determine which files are valid.
convertCamelCase(String, String) - Static method in class info.bioinfweb.commons.text.StringUtils
Converts a camel case keyword to a string with the specified separator where all characters are in lower case.
CookieManager - Class in info.bioinfweb.commons.servlet
 
CookieManager() - Constructor for class info.bioinfweb.commons.servlet.CookieManager
 
copy(InputStream, OutputStream) - Static method in class info.bioinfweb.commons.io.IOUtils
Copies data from an InputStream to an OutputStream.
copy(InputStream, OutputStream, boolean) - Static method in class info.bioinfweb.commons.io.IOUtils
Copies data from an InputStream to an OutputStream.
copy(InputStream, OutputStream, IOProgressListener) - Static method in class info.bioinfweb.commons.io.IOUtils
Copies data from an InputStream to an OutputStream.
copy(InputStream, OutputStream, boolean, IOProgressListener) - Static method in class info.bioinfweb.commons.io.IOUtils
Copies data from an InputStream to an OutputStream.
copy(File, File, IOProgressListener) - Static method in class info.bioinfweb.commons.io.IOUtils
Copies a file.
copy(File, File) - Static method in class info.bioinfweb.commons.io.IOUtils
Copies a file.
copyBits(long, long, long) - Method in interface info.bioinfweb.commons.collections.bitstorage.BitField
Copies the specified number of bits from one position in the bit field to another.
copyFromResource(String, OutputStream) - Static method in class info.bioinfweb.commons.io.IOUtils
Copies data from an InputStream to a OutputStream.
copyFromResource(String, OutputStream, IOProgressListener) - Static method in class info.bioinfweb.commons.io.IOUtils
Copies data from an InputStream to a OutputStream.
CountableSequenceView - Interface in info.bioinfweb.commons.bio.biojava3.core.sequence.views
Should be implemented by all sequence views that e.g.
countChangedCompounds() - Method in interface info.bioinfweb.commons.bio.biojava3.core.sequence.views.CountableSequenceView
 
countChangedCompounds() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ReplaceNucleotideSequenceView
 
countChangedCompounds() - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.UpperCaseSequenceView
 
countCompounds(C...) - Method in class info.bioinfweb.commons.bio.biojava3.core.sequence.views.ConcatenatedSequenceView
 
createDecoratedListIterator(ListIterator<E>) - Method in class info.bioinfweb.commons.collections.ListDecorator
 
createEntry() - Method in class info.bioinfweb.commons.servlet.CaptchaDBManagement
 
createFont(double) - Method in class info.bioinfweb.commons.graphics.ZoomableFont
Creates a new Font instance according to the properties if this object and the provided zoom factor.
createID(Connection, String, String, int, int) - Static method in class info.bioinfweb.commons.sql.IDGenerator
Returns a random ID which is not contained in the specified column of the specified table by the time this method is called.
createID(Connection, String, String, long, long) - Static method in class info.bioinfweb.commons.sql.IDGenerator
Returns a random ID which is not contained in the specified column of the specified table by the time this method is called.
createID(Connection, String, String, String, int) - Static method in class info.bioinfweb.commons.sql.IDGenerator
Returns a random ID which is not contained in the specified column of the specified table by the time this method is called.
createIntListCond(String, List<Integer>, String) - Static method in class info.bioinfweb.commons.sql.SQLUtils
 
createLabelTable(int, int, double) - Method in class info.bioinfweb.commons.swing.DecimalInput
 
createNewID() - Method in class info.bioinfweb.commons.IntegerIDManager
Returns a new sequence identifier that has not been returned before.
createNewID() - Method in class info.bioinfweb.commons.LongIDManager
Returns a new sequence identifier that has not been returned before.
createNextID(Connection, String, String, boolean, int) - Static method in class info.bioinfweb.commons.sql.IDGenerator
Returns the next ID which is not already present in the specified table.
createNextID(Connection, String, String, boolean, long) - Static method in class info.bioinfweb.commons.sql.IDGenerator
Returns the next ID which is not already present in the specified table.
createRedoAction(UndoableEdit) - Method in class info.bioinfweb.commons.swing.AbstractUndoActionManagement
 
createUndoAction(UndoableEdit) - Method in class info.bioinfweb.commons.swing.AbstractUndoActionManagement
 
createURI(String) - Static method in class info.bioinfweb.commons.swing.actions.OpenWebsiteAction
 
cutEnd(CharSequence, int) - Static method in class info.bioinfweb.commons.text.StringUtils
Cuts off the specified number of characters from the end of the specified character sequence.
cutEnd(String, int) - Static method in class info.bioinfweb.commons.text.StringUtils
Cuts off the specified number of characters from the end of the specified string.
CYTOSINE_INDEX - Static variable in class info.bioinfweb.commons.bio.AmbiguityBaseScore
 
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